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Computational Biology

Coding skills

Disclaimer

Made with the R package pagedown.

The source code is available on my datadrivencv-academic repository.

Last updated on 2023-03-09.

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Xabier Vázquez-Campos, PhD

Computational biologist | Environmental microbiologist

Education

PhD in Environmental Engineering

The University of New South Wales

Sydney, Australia

2015 - 2011

  • Thesis: “Geomicrobiological aspects of the (bio)leaching of weathered low-grade uranium ore”.

MSc in Microbiology

Autonomous University of Madrid

Madrid, Spain

2008 - 2007

  • Thesis: “Set-up of molecular ecology methodologies for the monitoring of microbial populations in an indirect reactor for the bioleaching of Zn from polymetallic sulfide concentrates” [in Spanish].

Licenciate in Biology

University of Vigo

Vigo, Spain

2007 - 2002

Research Experience

Visiting fellow

School of Biotechnology and Biomolecular Sciences

The University of New South Wales

Current - 2023

Senior research associate / Postdoctoral fellow

NSW Systems Biology Initiative. School of Biotechnology and Biomolecular Sciences

The University of New South Wales

2022

Research associate / Postdoctoral fellow

NSW Systems Biology Initiative. School of Biotechnology and Biomolecular Sciences

The University of New South Wales

2021 - 2017

Research associate / Postdoctoral fellow

BioGEMS group. Water Research Centre and School of Civil and Environmental Engineering

The University of New South Wales

2017 - 2015

Research assistant (casual)

BioGEMS group, School of Civil and Environmental Engineering

The University of New South Wales

2011

Research assistant

Bioprocesses Group, Faculty of Chemistry

University of Vigo

2011 - 2010

Research assistant

Bioprocesses Group, Faculty of Chemistry

University of Vigo

2007 - 2006

Teaching assistant

Faculty of Biology

University of Vigo

2006

Teaching Experience

Courses

CVEN9855 - Water & Wastewater Analysis

School of Civil and Environmental Engineering.

The University of New South Wales

2020

Invited lectures

Uranium heap leaching: Microbiological aspects

School of Civil and Environmental Engineering.

The University of New South Wales

2012

Workshops

EMBL-ABR: Phylogenetic trees for beginners

EMBL-ABR (Sydney node).

The University of New South Wales

2019

  • Node organiser and facilitator.

EMBL-ABR: Implementing Scalable Bioinformatic Workflows in Snakemake & Nextflow

EMBL-ABR (Sydney node).

The University of New South Wales

N/A

  • Facilitator.

EMBL-ABR: 16S Metagenomics with Galaxy Australia

EMBL-ABR (Sydney node).

University of Sydney

2018

  • Facilitator.

Long-read Data Analysis Workshop

NSW Systems Biology Initiative.

The University of New South Wales

N/A

  • Organiser, trainer, facilitator.

Hands on Zotero, a free alternative to EndNote

Bioprocesses group.

University of Vigo

2011

  • Organiser, sole trainer.

Supervision

Kevin Yonathan

PhD. Role: External supervisor.

University of Technology, Sydney

Current - 2019

Study of the response of microbial communities to silver nanoparticles through metagenomics.

I have also informally supervised, supported, mentored, or collaborated with a total of 21 students across multiple levels (1 Course project, 7 Honours, 12 PhD, and 1 Practicum).

Grants

Bioplatforms Australia / NSW Department of Industry RAAP – NCRIS NSW Co-investment Support Shared Grant

N/A

School of Biotechnology and Biomolecular Sciences / Ramaciotti Centre for Genomics at
The University of New South Wales

2021 - 2020

  • Total amount: AU$600,000

BABS sequencing grant

Investigation of a phage capable of species cross-infection

School of Biotechnology and Biomolecular Sciences / Ramaciotti Centre for Genomics at
The University of New South Wales

2020

  • AU$5,000 for sequencing

ResTech Support Scheme

OTUreporter pipeline coding project

The University of New South Wales

2020 - 2019

  • AU$15,000

Postdoctoral writing Fellowship Grant

N/A

School of Civil and Environmental Engineering at The University of New South Wales

2015

  • 0.4 FTE salary for 12 weeks

UNSW Tuition fee scholarship

N/A

Graduate Research School at The University of New South Wales

2015 - 2011

  • Tuition fees for PhD program

Australian Postgraduate Award (Industry)

N/A

Australian Federal Government

2015 - 2011

  • AU$27,651.00 per year for 3.5 years

Awards

SRAP Laureate 2020

N/A

Spanish Researchers in Australia-Pacific

2020

Publications

Selected peer-reviewed publications (5 out of 17). For a full list of my publications, including pre-prints and manuscripts under review, please consult my long-format CV.

Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by ‘Candidatus Formimonas warabiya’ strain DCMF

Frontiers in Microbiology 13, 1035247.

N/A

2022

S. I. Holland, X. Vázquez-Campos, E. Haluk, R. J. Edwards, M. J. Manefield & M. Lee.

Community-led, integrated, reproducible multi-omics with anvi’o

Nature Microbiology 6(1), 3-6.

N/A

2021

A. M. Eren, E. Kiefl, A. Shaiber, I. Veseli, S. E. Miller, M. S. Schechter, I. Fink, J. N. Pan, M. Yousef, E. C. Fogarty, F. Trigodet, A. R. Watson, Ö. C. Esen, R. M. Moore, Q. Clayssen, M. D. Lee, V. Kivenson, E. D. Graham, B. D. Merrill, A. Karkman, D. Blankenberg, J. M. Eppley, A. Sjödin, J. J. Scott, X. Vázquez-Campos, L. J. McKay, E. A. McDaniel, S. L. Stevens, R. E. Anderson, J. Fuessel, A. Fernandez-Guerra, L. Maignien, T. O. Delmont & A. D. Willis.

Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes

The ISME Journal 12, 2619-2639.

N/A

2018

H. L. Wong, R. A. White III, P. T. Visscher, J. C. Charlesworth, X. Vázquez-Campos & B. P. Burns.

Uranium binding mechanisms of the acid-tolerant fungus Coniochaeta fodinicola

Environmental Science & Technology 49(14), 8487-8496.

N/A

2015

X. Vázquez-Campos, A. S. Kinsela, R. N. Collins, B. A. Neilan, N. Aoyagi & T. D. Waite.

Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine inhabiting Ascomycota fungi from northern Australia

Mycologia 106(6), 1073-1089.

N/A

2014

X. Vázquez-Campos, A. S. Kinsela, T. D. Waite, R. N. Collins & B. A. Neilan.

Conference contributions

Selected abstracts presented at conferences (5 out of 10, including 3 oral presentation and 7 posters).

I have also contributed to 21 abstracts presented by co-authors at conferences.

Unusual DPANN Archaea from a radioactive legacy site

Australian Microbial Ecology Conference (AusME 2019).

Perth, WA, Australia

2019

X. Vázquez-Campos, A. S. Kinsela, M. W. Bligh, M. R. Wilkins, T. E. Payne & T. D. Waite [oral presentation].

OTUreporter: an automated pipeline for the analysis and report of amplicon sequencing data

ABACBS-2018 National Conference.

Melbourne, VIC, Australia

2018

X. Vázquez-Campos, A. Chilton, J. Koval, J. J. Tree & M. R. Wilkins [poster].

New Archaea lineages from a radioactive legacy site

Molecular biology of archaea: From mechanisms to ecology (MoBA6).

Vienna, Austria

N/A

X. Vázquez-Campos, A. S. Kinsela, M. W. Bligh, M. R. Wilkins, T. E. Payne & T. D. Waite [poster].

Metagenomic and geochemical changes following rainfall at a legacy radionuclide waste disposal site

Australian Microbial Ecology Conference (AusME 2017).

Melbourne, VIC, Australia

2017

X. Vázquez-Campos, A. S. Kinsela, T. E. Payne & T. D. Waite [oral presentation].

Rainfall-mediated biogeochemical changes at a legacy radionuclide waste disposal site

16th International Symposium on Microbial Ecology (ISME16).

Montreal, Canada

2016

X. Vázquez-Campos, A. S. Kinsela, J. J. Harrison, K. Wilsher, S. Thiruvoth, B. Rowling, T. E. Payne & T. D. Waite [poster].

Service

Institutional Service

  • University of New South Wales
    • Postgraduate student representative at the OH&S Committee of the School of Civil and Environmental Engineering (2013–2015).

N/A

Professional Affiliations

  • American Society for Microbiology
    • Regular member (2015–Current).
  • Australian Bioinformatics and Computational Biology Society
    • Regular member (2018–Current).
  • Australian Society for Microbiology
    • Regular member (2015–Current).
  • International Society for Microbial Ecology
    • Regular member (2014–Current).
  • Spanish Researchers in Australia-Pacific
    • Co-founder (2014).
    • Board member and web/IT coordinator (2014–2020).
    • Regular member (2021–Current).

N/A

Conferences

  • Australian Microbial Ecology conference 2022 (AusME2022)
    • Plenary chair and poster judge (2022).
  • 6th Australia-Spain Research Forum: Big Data
    • Event registration (2020).
  • 5th Australia-Spain Research Forum: 5 years Bridging Australia and Spain in Research and Academia
    • Website (2019).
  • 4th Australia-Spain Research Forum: Earth
    • Website (2018).
  • 3rd Australia-Spain Research Forum: Air
    • Website and event registration (2017).
  • 2nd Australia-Spain Research Forum: Light
    • Website (2016).
  • Australia-Spain Water Forum
    • Website and event photography (2015).

N/A

Peer Reviews

Reviewer for >10 different journals since 2016, including leading journals in their own fields, e.g., Astrobiology, Environmental Science and Technology, or Microbiome.

N/A

N/A

For a full record as reviewer, consult my public ResearcherID profile.